How can I convert a file with the command line?
According to the wiki, it is possible to convert (link is just an example, not specific to the formats you mentioned) via the command line. However, I'm not so certain (seeing as I haven't tested this) if you can convert between non-native formats.

I believe you would need to use the script to import VRML, then subsequently the script to export FBX.

If you are looking to automate the process, you could write a script that runs these commands sequentially:

#!/bin/sh
exec blender foobar.vrml --background --python name_of_import_plugin.py -- foobar.blend
exec blender foobar.blend --background --python name_of_fbx_export_plugin.py foobar.fbx


Please note you'd need to edit the above code, and I have not tested this, but in theory it should work.